Comparative Investigations of the Sandfish’s β-Keratin (Reptilia: Scincidae: Scincus scincus). Part 1: Surface and Molecular Examinations

2012 ◽  
Vol 15 ◽  
pp. 1-16 ◽  
Author(s):  
Konrad Staudt ◽  
Friederike Petra Maria Saxe ◽  
Heiko Schmied ◽  
Raphael Soeur ◽  
Wolfgang Böhme ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemical Composition ◽  
Protein Sequence ◽  
Micro Structure ◽  
Low Friction ◽  
Desert Sand ◽  
Glycosylation Sites ◽  
Keratin Proteins ◽  
Reptilian Species ◽  
Scincus Scincus

The Sandfish (Scincidae: Scincus Scincus) Is a Lizard Capable of Moving through Desert Sand in a Swimming-Like Fashion. the Epidermis of this Lizard Shows a High Resistance against Abrasion Together with a Low Friction to Sand as an Adaption to a Subterranean Life below the Desert’s Surface, Outperforming even Steel. the Low Friction Is Mainly Caused by Chemical Composition of the Scales, which Consist of Glycosylated β-Keratins. in this Study, the Friction, the Micro-Structure, the Glycosylation of the β-Keratin Proteins and β-Keratin Coding DNA of the Sandfish in Comparison to other Reptilian Species Was Investigated, Mainly with the Closely Related Berber Skink (Scincidae: Eumeces Schneideri) and another Sand Swimming Species, the Not Closer Related Shovel-Snouted Lizard (Lacertidae: Meroles Anchietae). Glycosylated β-Keratins of the Sandfish, Visualized with Different Lectins Resulted in O-Linked Glycans through PNA Employed as Carbohydrate Marker. Furthermore, the Glycosylation of β-Keratins in Various Squamatean Species Was Investigated and All Species Tested Were Found Positive; however, it Seems Like both Sand Swimming Species Examined Have a much Stronger Glycosylation of their β-Keratins. in Order to Prove this Finding through a Genetic Foundation, DNA of a β-Keratin Coding Gene of the Sandfish Was Sequenced and Compared with a Homologue Gene of Eumeces Schneideri. by Comparison of the Protein Sequence, a Higher Abundance of O-Glycosylation Sites Was Found in the Sandfish (enabled through the Amino Acids Serine and Threonine), Giving Molecular Support for a Higher Glycosylation of the β-Keratins in this Species.

scholarly journals Comparative Analyses of ACE2 Receptor Binding Corona Viruses that Cause Mild versus Severe Acute Respiratory Syndrome in Humans

2021 ◽  
pp. 64-85
Author(s):  
Peramachi Palanivelu
Keyword(s):  
Amino Acids ◽  
Severe Acute Respiratory Syndrome ◽  
Receptor Binding ◽  
Metal Binding ◽  
Protein Sequence ◽  
Active Sites ◽  
Protein Sequence Analysis ◽  
X Ray ◽  
Glycosylation Sites ◽  
Spike Proteins

Aim: To analyze the spike proteins and Replication-Transcription Complexes (RTCs) of the Mild and Severe Acute Respiratory Syndrome (SARS) and SARS-related coronaviruses (CoVs) to find out the similarities and differences between them, as both of groups bind to angiotensin-converting enzyme 2 (ACE2) receptor for human cell entry. Study Design: Bioinformatics, Biochemical, Site-Directed Mutagenesis (SDM), X-ray crystallographic, cryo-Electron microscopic (cryo-EM) and Mass Spectrometric (MS) data were analyzed. Methodology: The protein sequence data for spike proteins and the proteins of the RTCs, viz. the RNA- dependent RNA polymerases (RdRps), primases and the nonstructural protein 7 (NSP7) were obtained from PUBMED and SWISS-PROT databases. The advanced version of Clustal Omega was used for protein sequence analysis. Along with the conserved motifs identified by the bioinformatics analysis, the data already available by biochemical and SDM experiments and X-ray crystallographic and cryo-EM  studies on these  proteins were used to confirm the possible amino acids involved in ACE2 receptor binding and active sites of the RTCs. For identification of probable N-linked and O-linked glycosylation sites, NetNGlyc 1.0 and NetOGlyc 4.0 tools of Technical University of Denmark were used. ExPASy tool was used for pI analysis. Results: The spike protein of human CoV (HCoV)-NL63 is ~90 amino acids longer than the spike proteins of SARS and SARS-related CoVs. The additions are mostly found in the N-terminal regions and few insertions are also found in the crucial receptor binding domain (RBD). The SARS and SARS-related CoVs and HCoV-NL63 showed several conserved residues, motifs and large peptide regions. The most important aspect between the recent pandemic causing SARS-CoV-2 and HCoV-NL63 is a unique but different tetrapeptide insertions very close to the S1/S2 cleavage region, i.e., -PRRA-  and  -IPVR-, respectively. The next cleavage point S2’ and the transmembrane domains are conserved between the two groups. The RdRps are highly conserved between the two groups. The catalytic regions, catalytic amino acids and the NTP selection tripeptide regions are completely conserved between SARS-CoVs and HCoV-NL63.  However, one of the metal binding sites, viz. the universal –GDD- reported in all RdRps is aligning with– KDG- in the RdRp of HCoV-NL63. The other metal binding site, viz. –SDD- is completely conserved in both the groups. The NiRAN domains of the RdRps differed from the possible catalytic amino acid and NTP selection tripeptide regions. The primases (NSP8) and the NSP7 subunits of the RTC are highly conserved in both the groups. The NSP8 and NSP7 subunits exhibit closer similarities between the MERS-CoV and HCoV-NL63. Unlike other SARS and SARS-related CoVs, the HCoV-NL63 possesses only a single accessory protein. Interestingly, a large number of amino acids are replaced with Ns in the spike proteins (which is also reflected in the number of N-linked glycosylation sites in it) as well as in the RTC. Conclusions: Detailed analysis revealed several unique features in the HCoV-NL63 pathogen. As all the pandemic strains like SARS-CoV-1, SARS-CoV-2 and the milder HCoV-NL63 strain, use the same ACE2 receptor for entry into human cells, the frequent infection of humans by HCoV-NL63, especially in children, suggests that there is an ample opportunity for highly pathogenic variants to evolve in the future.

Nglyc: A Random Forest Method for Prediction of N-Glycosylation Sites in Eukaryotic Protein Sequence

2020 ◽  
Vol 27 (3) ◽  
pp. 178-186 ◽  
Author(s):  
Ganesan Pugalenthi ◽  
Varadharaju Nithya ◽  
Kuo-Chen Chou ◽  
Govindaraju Archunan
Keyword(s):  
Random Forest ◽  
Protein Sequence ◽  
Glycosylation Site ◽  
Computational Method ◽  
The Other ◽  
Eukaryotic Protein ◽  
Random Forest Method ◽  
Glycosylation Sites ◽  
Human And Mouse ◽  
Better Than

Background: N-Glycosylation is one of the most important post-translational mechanisms in eukaryotes. N-glycosylation predominantly occurs in N-X-[S/T] sequon where X is any amino acid other than proline. However, not all N-X-[S/T] sequons in proteins are glycosylated. Therefore, accurate prediction of N-glycosylation sites is essential to understand Nglycosylation mechanism. Objective: In this article, our motivation is to develop a computational method to predict Nglycosylation sites in eukaryotic protein sequences. Methods: In this article, we report a random forest method, Nglyc, to predict N-glycosylation site from protein sequence, using 315 sequence features. The method was trained using a dataset of 600 N-glycosylation sites and 600 non-glycosylation sites and tested on the dataset containing 295 Nglycosylation sites and 253 non-glycosylation sites. Nglyc prediction was compared with NetNGlyc, EnsembleGly and GPP methods. Further, the performance of Nglyc was evaluated using human and mouse N-glycosylation sites. Results: Nglyc method achieved an overall training accuracy of 0.8033 with all 315 features. Performance comparison with NetNGlyc, EnsembleGly and GPP methods shows that Nglyc performs better than the other methods with high sensitivity and specificity rate. Conclusion: Our method achieved an overall accuracy of 0.8248 with 0.8305 sensitivity and 0.8182 specificity. Comparison study shows that our method performs better than the other methods. Applicability and success of our method was further evaluated using human and mouse N-glycosylation sites. Nglyc method is freely available at https://github.com/bioinformaticsML/ Ngly.

scholarly journals Phytochemical and Psychotropic Research of Motherwort (Leonurus cardiaca L.) Modified Dry Extracts

Plants ◽  
2021 ◽  
Vol 10 (2) ◽  
pp. 230
Author(s):  
Oleh Koshovyi ◽  
Ain Raal ◽  
Igor Kireyev ◽  
Nadiya Tryshchuk ◽  
Tetiana Ilina ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemical Composition ◽  
Phenolic Compounds ◽  
Pharmacological Activity ◽  
Ellagic Acid ◽  
Hydroxycinnamic Acids ◽  
Psychotropic Activity ◽  
Phytochemical Analysis ◽  
Phenolic Substances ◽  
Leonurus Cardiaca

The prospect of creating a new medicine with psychotropic activity is shown as a result of studying the chemical composition and pharmacological activity of modified dry extracts of motherwort (Leonurus cardiaca L.) tincture. The most promising substances were the dry extracts, modified by adding small amounts of arginine, valine, phenylalanine, glycine, lysine, and alanine. A total of 15 main phenolic substances were found in the extracts, and eight of them were identified. There were also 10 hydroxycinnamic acids in these extracts, three of which were identified (chlorogenic, caffeic, and rosmarinic acids). The dominant hydroxycinnamic acids were chlorogenic and caffeic acids. Among flavonoids, catechin, hyperoside, and rutin were identified. It should be noted that the extracts had a significant content of ellagic acid. On the basis of the results of the phytochemical analysis of the extracts, it can be concluded that the composition of phenolic compounds does not differ significantly, and the main differences are related to amino acids, which obviously have an impact on the overall pharmacological effect. The results obtained indicate the presence of anxiolytic activity in the motherwort extracts studied in complex with amino acids. The extracts with glycine, valine, and arginine were more effective in reducing anxiety in animals.

scholarly journals Chemical composition and nutritional quality of short-ripened rennet cheeses produced by traditional methods

2018 ◽  
Vol 74 (10) ◽  
pp. 5971-2018 ◽  
Author(s):  
PRZEMYSŁAW KNYSZ ◽  
MICHAŁ GONDEK ◽  
RENATA PYZ-ŁUKASIK ◽  
MONIKA ZIOMEK ◽  
ŁUKASZ DROZD ◽  
...  
Keyword(s):  
Amino Acids ◽  
Amino Acid ◽  
Chemical Composition ◽  
G Protein ◽  
Nutritive Value ◽  
Salt Content ◽  
Amino Acid Content ◽  
Traditional Methods ◽  
Dairy Starter Cultures ◽  
Limiting Amino Acids

The aim of the study was to determine the variability in the chemical composition and nutritive value parameters of smoked and unsmoked short-ripened rennet cheeses and unsmoked long-ripened rennet cheeses produced by traditional methods. The raw material for the production of short-ripened cheeses was pasteurized cows’ milk obtained from a dairy, whereas the long-ripened cheeses were manufactured from raw cows’ milk obtained from the producer’s farm. All three varieties of cheese examined were produced with commercial dairy starter cultures. The material for the study was collected in winter, directly at the producers’ retail outlets in southern and eastern Poland. The basic chemical composition was determined according to the Polish Standards, whereas the amino acid profiles of proteins from the cheeses were determined by ion-exchange chromatography. The result analysis revealed significant differences between the different varieties of cheese in terms of their water content, ranging from 32.2% to 42.1%, as well as protein content, which varied from 25.6% to 31.6%. Fat levels ranged between 22.2% and 24%, whereas total ash content amounted to 5.1-5.8%. The significantly highest salt content was found in unsmoked short-ripened cheeses. In all three cheese varieties, the total exogenous amino acid content was comparable, ranging from 46.17 g to 47.36 g/100 g protein, and that of endogenous amino acids varied from 52 g to 53 g/100 g protein. The biological value of proteins was determined by calculating to the chemical score (CS), as described by Mitchell and Block, and the essential amino acid index (EAAI), as described by Oser. A comparison of the results with the standard chicken egg white proteins showed that the limiting amino acids for all varieties of cheese were methionine and cysteine. On the other hand, a comparison with the FAO/WHO-suggested pattern of amino acid requirements (1991) for all age groups over 1 year of age showed that the limiting amino acids were methionine and cysteine in smoked and unsmoked short-ripened cheeses, and treonine in long-ripened cheeses. Considering the chemical indices, such as CS and EAAI, it may be concluded that the traditional rennet cheeses produced in southern and eastern Poland have a favourable amino acid composition of proteins and a high nutritive value..

scholarly journals Rapeseed protein-fibre concentrate: chemical composition and functional properties

2018 ◽  
Vol 117 (4) ◽  
pp. 86-99
Author(s):  
Anna Ostrowska ◽  
Magdalena Kozłowska ◽  
Danuta Rachwał ◽  
Piotr Wnukowski ◽  
Ewa Nebesny ◽  
...  
Keyword(s):  
Amino Acids ◽  
Chemical Composition ◽  
Functional Properties ◽  
Dietary Fibre ◽  
Research Study ◽  
Essential Amino Acids ◽  
Absorption Capacity ◽  
Food Ingredient ◽  
Rapeseed Protein ◽  
Functional Features

Dietary fibre has a beneficial effect on human health that is manifested, among other things, in a reduced risk of obesity, diabetes or neoplasms. Its numerous functional properties render it a desirable food additive. The objective of the research study was to assess the nutritional and functional properties of a novel rapeseed protein-fibre concentrate (RPFC) developed by a NapiFeryn BioTech company. The chemical composition, including the amino acid composition, and the functional properties of RPFC were compared with those of the soy fibre (SF) and pea fibre (PF) available on the market; the purpose of the comparison was to evaluate the potential of RPFC as a novel ingredient for use in food applications. The research study showed that RPFC contained significantly more protein than SF and PF. At the same time it was found that the level of total dietary fibre in RPFC was similar to the level of this ingredient in SF. What's more, RPFC was characterized by the highest contents of ash and phytic acid. Based on the analysis results of amino acids it was proved that the level of lysine was the highest in RPFC. The RPFC was characterized by a higher content of essential amino acids than PF and a lower content thereof than SF. RPFC was distinguished by good functional features, such as emulsifying activity, emulsion stability, and water and oil absorption capacity. It was showed that RPFC had suitable features to be used as a functional food ingredient in food products.

CHEMICAL COMPOSITION OF HYPHAL AND SCLEROTIAL WALLS OF SCLEROTIUM ROLFSII SACC.

1967 ◽  
Vol 13 (2) ◽  
pp. 137-141 ◽  
Author(s):  
I. Chet ◽  
Y. Henis ◽  
R. Mitchell
Keyword(s):  
Amino Acids ◽  
Chemical Composition ◽  
Acid Hydrolysis ◽  
Sclerotium Rolfsii ◽  
Ash Content ◽  
Chemical Degradation ◽  
Chemical Components

The chemical components of the sclerotial and hyphal walls of the fungus Sclerotium rolfsii Sacc. are compared. Sclerotial walls contain a melanin-like pigment which is absent from hyphal walls. They are also higher in non-hydro-lyzable residue, in lipids, and in ash content. In both walls, glucose, mannose, and glucosamine are found after acid hydrolysis. Acid hydrolysates of sclerotial and hyphal walls contain 10 and 13 amino acids, respectively, L-arginine, L-serine, and L-proline being absent from sclerotial walls. The possible role of some of these components in the resistance of the sclerotia to biological and chemical degradation is discussed.

Microstructure and Mechanical Properties of High Strength Low Alloy Steel Q550D

2021 ◽  
Vol 1035 ◽  
pp. 424-429
Author(s):  
Fang Po Li ◽  
Ning Li ◽  
Xian Lin Wang ◽  
Ming Hua Liang
Keyword(s):  
Mechanical Properties ◽  
Chemical Composition ◽  
Oil And Gas ◽  
High Strength ◽  
Service Performance ◽  
Low Alloy Steel ◽  
Micro Structure ◽  
Gas Drilling ◽  
Drilling Equipment ◽  
Equipment Manufacture

Drilling equipment is the key of oil and gas drilling development. Its manufacturing quality and service performance have important influence on oil and gas drilling development safety. The application of high strength grade steel plays an important role in improving drilling equipment manufacturing level and service performance. In this paper, the chemical composition, microstructure, tensile properties, impact properties and hardness of TMCP Q550D and Q-T Q550D high-strength low-alloy steel were tested and compared, and the application feasibility for drilling equipment manufacture was analyzed comprehensively. The experimental results show that the mechanical properties of Q550D by two different methods were obviously higher than the requirement of national standard. Q550D steel had excellent plasticity and toughness, which meets the requirement of drilling equipment manufacture. The main difference between different steel lied in their chemical composition and micro-structure. Carbon content of TMCP Q550D steel plate was lower than that of QT Q550D, and TMCP Q550 was mainly depend on TMCP technology and micro-alloy elements, whose micro-structure was mainly granular bainite. Q-T Q550D was mainly depend on Q-T technology, and its microstructure was tempered sorbite with obvious banded structure and slightly low toughness.

Complete sequence and in vitro expression of a tissue-specific phosphatidylinositol-linked N-CAM isoform from skeletal muscle

Development ◽  
1988 ◽  
Vol 104 (1) ◽  
pp. 165-173 ◽  
Author(s):  
C.H. Barton ◽  
G. Dickson ◽  
H.J. Gower ◽  
L.H. Rowett ◽  
W. Putt ◽  
...  
Keyword(s):  
Skeletal Muscle ◽  
Amino Acids ◽  
Cell Surface ◽  
Protein Sequence ◽  
Single Copy ◽  
In Vitro Transcription ◽  
Full Length ◽  
Covalent Attachment ◽  
Size Difference

Neural cell adhesion molecules (N-CAMs) are a family of cell surface sialoglycoproteins encoded by a single copy gene. A full-length cDNA clone that encodes a nontransmembrane phosphatidylinositol (PI) linked N-CAM of Mr 125 × 10(3) has been isolated from a human skeletal muscle cDNA library. The deduced protein sequence encodes a polypeptide of 761 amino acids and is highly homologous to the N-CAM isoform in brain of Mr 120 × 10(3). The size difference between the 125 × 10(3). The size difference between the 125 × 10(3) Mr skeletal muscle form and the 120 × 10(3) Mr N-CAM form from brain is accounted for by the insertion of a block of 37 amino acids called MSD1, in the extracellular domain of the muscle form. Transient expression of the human cDNA in COS cells results in cell surface N-CAM expression via a putative covalent attachment to PI-containing phospholipid. Linked in vitro transcription and translation experiments followed by immunoprecipitation with anti-N-CAM antibodies demonstrate that the full-length clone of 761 amino acid coding potential produces a core polypeptide of Mr 110 × 10(3) which is processed by microsomal membranes to yield a 122 × 10(3) Mr species. Taken together, these results demonstrate that the cloned cDNA sequence encodes a lipid-linked, PI-specific phospholipase C releasable surface isoform of N-CAM with core glycopeptide molecular weight corresponding to the authentic muscle 125 × 10(3) Mr N-CAM isoform. This is the first direct correlation of cDNA and deduced protein sequence with a known PI-linked N-CAM isoform from skeletal muscle.

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